MOACO Biclustering of gene expression data

Many bioinformatics data sets come from DNA microarray experiments. Biclustering of gene expression data can identify genes with similar behaviour with respect to different conditions. Ant Colony Optimisation (ACO) algorithms have been shown to be effective problem solving strategies for a wide range of problem domains. Multiple Objective Ant Colony Optimisation (MOACO) mainly focuses on solving the multiple objective combinatorial optimisation problems. This paper incorporates crowding update technology into MOACOB and proposes crowding MOACO biclustering algorithm to mine biclusters from gene expression data. Experimental results are shown for biclustering algorithm on two real gene expression data.

[1]  Daniel Angus,et al.  Niching ant colony optimisation , 2008 .

[2]  Fabrício Olivetti de França,et al.  bicACO: An Ant Colony Inspired Biclustering Algorithm , 2008, ANTS Conference.

[3]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[4]  Luca Maria Gambardella,et al.  MACS-VRPTW: a multiple ant colony system for vehicle routing problems with time windows , 1999 .

[5]  Prospero C. Naval,et al.  An effective use of crowding distance in multiobjective particle swarm optimization , 2005, GECCO '05.

[6]  Kathleen Marchal,et al.  Adaptive quality-based clustering of gene expression profiles , 2002, Bioinform..

[7]  Krista Rizman Zalik,et al.  Biclustering of gene expression data , 2005 .

[8]  Marco Laumanns,et al.  Combining Convergence and Diversity in Evolutionary Multiobjective Optimization , 2002, Evolutionary Computation.

[9]  Daniel Angus,et al.  Multiple objective ant colony optimisation , 2009, Swarm Intelligence.

[10]  Thomas Stützle,et al.  Ant Colony Optimization , 2009, EMO.

[11]  D Haussler,et al.  Knowledge-based analysis of microarray gene expression data by using support vector machines. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Michael Guntsch,et al.  Applying Population Based ACO to Dynamic Optimization Problems , 2002, Ant Algorithms.

[13]  Inderjit S. Dhillon,et al.  Co-clustering documents and words using bipartite spectral graph partitioning , 2001, KDD '01.

[14]  Thomas Stützle,et al.  Parallel Ant Colony Optimization for the Traveling Salesman Problem , 2006, ANTS Workshop.

[15]  Zhoujun Li,et al.  Multi-objective ant colony optimization biclustering of microarray data , 2009, 2009 IEEE International Conference on Granular Computing.

[16]  Marco Dorigo,et al.  Ant colony optimization for continuous domains , 2008, Eur. J. Oper. Res..

[17]  Marco Dorigo,et al.  Ant colony optimization theory: A survey , 2005, Theor. Comput. Sci..

[18]  Philip S. Yu,et al.  Enhanced biclustering on expression data , 2003, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings..

[19]  Bart De Moor,et al.  Biclustering microarray data by Gibbs sampling , 2003, ECCB.

[20]  Ronald W. Davis,et al.  A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.

[21]  Federico Divina,et al.  A multi-objective approach to discover biclusters in microarray data , 2007, GECCO '07.

[22]  J. Mesirov,et al.  Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Francisco Herrera,et al.  A taxonomy and an empirical analysis of multiple objective ant colony optimization algorithms for the bi-criteria TSP , 2007, Eur. J. Oper. Res..

[24]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Daniel Angus,et al.  Niching for Population-Based Ant Colony Optimization , 2006, 2006 Second IEEE International Conference on e-Science and Grid Computing (e-Science'06).

[26]  Sushmita Mitra,et al.  Multi-objective evolutionary biclustering of gene expression data , 2006, Pattern Recognit..

[27]  Christine Solnon,et al.  Ants can solve constraint satisfaction problems , 2002, IEEE Trans. Evol. Comput..

[28]  Padraig Cunningham,et al.  Biclustering of expression data using simulated annealing , 2005, 18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05).

[29]  Kenneth Alan De Jong,et al.  An analysis of the behavior of a class of genetic adaptive systems. , 1975 .

[30]  Martin Middendorf,et al.  A Population Based Approach for ACO , 2002, EvoWorkshops.

[31]  Kalyanmoy Deb,et al.  A fast and elitist multiobjective genetic algorithm: NSGA-II , 2002, IEEE Trans. Evol. Comput..

[32]  Daniel Angus,et al.  Crowding Population-based Ant Colony Optimisation for the Multi-objective Travelling Salesman Problem , 2007, 2007 IEEE Symposium on Computational Intelligence in Multi-Criteria Decision-Making.

[33]  Aidong Zhang,et al.  Cluster analysis for gene expression data: a survey , 2004, IEEE Transactions on Knowledge and Data Engineering.

[34]  Christine Solnon,et al.  A study of ACO capabilities for solving the maximum clique problem , 2006, J. Heuristics.

[35]  Abbas Afshar,et al.  MULTI-OBJECTIVE OPTIMIZATION OF TIME-COST-QUALITY USING MULTI-COLONY ANT ALGORITHM , 2007 .

[36]  Luca Maria Gambardella,et al.  Ant colony system: a cooperative learning approach to the traveling salesman problem , 1997, IEEE Trans. Evol. Comput..

[37]  Marco Dorigo Ant colony optimization , 2004, Scholarpedia.

[38]  Richard F. Hartl,et al.  An improved Ant System algorithm for theVehicle Routing Problem , 1999, Ann. Oper. Res..

[39]  Daniel Angus Niching for ant colony optimization , 2006 .

[40]  Thomas Stützle,et al.  MAX-MIN Ant System , 2000, Future Gener. Comput. Syst..

[41]  Roded Sharan,et al.  Discovering statistically significant biclusters in gene expression data , 2002, ISMB.

[42]  Arlindo L. Oliveira,et al.  Biclustering algorithms for biological data analysis: a survey , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[43]  George M. Church,et al.  Biclustering of Expression Data , 2000, ISMB.

[44]  Yuvraj Gajpal,et al.  Multi-ant colony system (MACS) for a vehicle routing problem with backhauls , 2009, Eur. J. Oper. Res..